Align Phosphoglucomutase/phosphomannomutase; PGM/PMM; EC 5.4.2.2; EC 5.4.2.8 (characterized)
to candidate WP_011973151.1 MAEO_RS02160 phosphoglucosamine mutase
Query= SwissProt::Q68BJ6 (456 letters) >NCBI__GCF_000017185.1:WP_011973151.1 Length = 452 Score = 309 bits (792), Expect = 1e-88 Identities = 178/466 (38%), Positives = 274/466 (58%), Gaps = 33/466 (7%) Query: 3 KLFGTFGVRGIANEEITPEFALKIGMAFGTLLKREGRERPLVVVGRDTRVSGEMLKDALI 62 KLFGT G+R + +TPE A K+G A + K VVVGRDTR +G++++++L Sbjct: 2 KLFGTSGIR---MKNLTPEIAYKVGFAVSQIAKN-------VVVGRDTRTTGDLIRNSLF 51 Query: 63 SGLLSTGCDVIDVGIAPTPAIQWATNHFNADGGAVITASHNPPEYNGIKLLEPNGMGLKK 122 +GLL+ G +++D+GI PTP + ++ ++ D G +ITASHNP EYNGIKL +G + Sbjct: 52 AGLLNGGAEIVDIGIVPTPTLGYSARNY--DMGIMITASHNPSEYNGIKLFNKDGTSFRP 109 Query: 123 EREAIVEELFFSE-DFHRAKWNEIGEL-RKEDIIKPYIEAIKNRVDVEAIKKRRPFVVVD 180 E+E +E++ +++ + R WN I ++ E +K Y + I + V++ + VVVD Sbjct: 110 EQEQNIEDIIYNKKNQKRVSWNSIKKVWTDESALKKYSDFILDSVEIN----KNFSVVVD 165 Query: 181 TSNGAGSLTLPYLLRELGCKVVSVNAHPDGHFPARNPEPNEENLKGFMEIVKALGAD--- 237 +N AG + PYL ++G V+SVN H DG F R+PEPNE+NL+ M ++K L + Sbjct: 166 CANSAGCVASPYLFTDVGAHVISVNGHIDGRFIGRSPEPNEKNLQDTMHMIKGLNENNKG 225 Query: 238 ---FGVAQDGDADRAVFIDENGRFIQGDKTFALVADAVLRENGGGLLVTTIATSNLLDDI 294 G+A DGDADR + IDE GR DK A+ + + + G ++TT+ S +++ Sbjct: 226 NKYIGIAHDGDADRMIAIDEKGRLTDFDKLLAVFSRYMAEKTGTKTIITTVDASMAIEEY 285 Query: 295 AKRNGAKVMRTKVGDLIVARALLENNGTI-GGEENGGVIFPDFVLGRDGAMTTAKIVEIF 353 K V+RTKVGD+ V+ L +++ I GGE +G I D L DG ++ +++E+ Sbjct: 286 LKDLNVNVIRTKVGDVAVSDELNKHDDAIFGGEPSGTWIHKDIHLTPDGILSGLRLLEMM 345 Query: 354 AKSGKKFSELIDELPKYYQFKTKRHVEGDRKAIVAKVAELAEKKG-----YKIDTTDGTK 408 KK ELID++P Y + K D+K I V + K G +++T DG + Sbjct: 346 EFYDKKLYELIDDVPCYSNLREKLPCPDDKKII---VMDFVIKNGENIFDAEVETIDGAR 402 Query: 409 IIFDDGWVLVRASGTEPIIRIFSEAKSEEKAREYLELGIKLLEEAL 454 DDGWVL+R SGTEP +R+ EAK++ A+E LE GIKL+++ L Sbjct: 403 FSLDDGWVLIRPSGTEPFVRVRVEAKNDIIAKELLEKGIKLVKDGL 448 Lambda K H 0.317 0.139 0.396 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 597 Number of extensions: 35 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 456 Length of database: 452 Length adjustment: 33 Effective length of query: 423 Effective length of database: 419 Effective search space: 177237 Effective search space used: 177237 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory